LAMMPS (8 Feb 2023)
Processor partition = 7
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
variable ibead uloop 8 pad

units           real
neigh_modify    delay 2 every 1

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic

pair_style      lj/charmm/coul/long 11 12
pair_modify     mix arithmetic
kspace_style    pppm 1e-4

read_data system.data
Reading data file ...
  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  8674 atoms
  reading velocities ...
  8674 velocities
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  18 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  5869 bonds
  reading angles ...
  3264 angles
  reading dihedrals ...
  708 dihedrals
  reading impropers ...
  38 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     9 = max # of 1-3 neighbors
    17 = max # of 1-4 neighbors
    21 = max # of special neighbors
  special bonds CPU = 0.004 seconds
  read_data CPU = 0.138 seconds
#read_restart    system_${ibead}.rest1
special_bonds   charmm

fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0

thermo          10
thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
timestep        0.08

# restart         100 system_${ibead}.rest1 system_${ibead}.rest2

group prot id <= 256
256 atoms in group prot
# dump 1 prot dcd 100 prot_${ibead}.dcd

run             200
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.22071363
  grid = 20 20 20
  stencil order = 5
  estimated absolute RMS force accuracy = 0.024910591
  estimated relative force accuracy = 7.5017505e-05
  using double precision KISS FFT
  3d grid and FFT values/proc = 15625 8000
Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 2 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
WARNING: Inconsistent image flags (src/domain.cpp:815)
Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
        10   11.858328     -24949.912     -24643.343      11.21746       379.42274     -589.42772    
        20   13.313433     -22332.782     -21988.595      25.891404      425.98075     -189.42618    
        30   14.492332     -18605.094     -18230.43       60.87232       463.70115      853.22726    
        40   10.100576     -15158.156     -14897.03       103.87947      323.18115      1870.5664    
        50   10.437976     -12976.762     -12706.913      161.50852      333.97672      2649.3283    
        60   10.544993     -11868.561     -11595.946      225.58416      337.40089      3264.9267    
        70   9.756396      -11851.23      -11599.002      303.66274      312.16868      3549.9084    
        80   10.642372     -12316.225     -12041.092      392.92619      340.51663      3853.3301    
        90   9.3834726     -12853.33      -12610.744      501.5373       300.2365       3943.7218    
       100   8.9858656     -13254.517     -13022.21       619.67563      287.51455      3852.5038    
       110   8.9674385     -13407.55      -13175.719      752.87088      286.92495      3047.0516    
       120   8.7200626     -13430.184     -13204.748      897.34682      279.00983      2614.6547    
       130   8.4404226     -13413.462     -13195.256      1051.1979      270.06239      2361.7563    
       140   8.1867868     -13405.663     -13194.013      1215.2723      261.94697      2042.4666    
       150   8.26024       -13427.11      -13213.561      1389.0864      264.29721      2179.5219    
       160   8.2139102     -13403.956     -13191.605      1573.9454      262.81482      2489.6486    
       170   8.2258918     -13367.291     -13154.631      1768.2198      263.19819      2793.6911    
       180   8.4548603     -13245.62      -13027.04       1968.4468      270.52434      3070.2942    
       190   8.4589955     -12920.954     -12702.268      2174.1321      270.65665      3360.4993    
       200   8.537811      -12448.973     -12228.248      2382.746       273.17846      3370.2077    
Loop time of 35.3334 on 1 procs for 200 steps with 8674 atoms

Performance: 0.039 ns/day, 613.428 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 27.709     | 27.709     | 27.709     |   0.0 | 78.42
Bond    | 0.13165    | 0.13165    | 0.13165    |   0.0 |  0.37
Kspace  | 2.4416     | 2.4416     | 2.4416     |   0.0 |  6.91
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.12826    | 0.12826    | 0.12826    |   0.0 |  0.36
Output  | 0.002116   | 0.002116   | 0.002116   |   0.0 |  0.01
Modify  | 4.863      | 4.863      | 4.863      |   0.0 | 13.76
Other   |            | 0.05754    |            |       |  0.16

Nlocal:           8674 ave        8674 max        8674 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          27366 ave       27366 max       27366 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 4485849
Ave neighs/atom = 517.16036
Ave special neighs/atom = 2.2573207
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:35
